Seperate mitochondria and other genome

[Febri Gunawan]

Hi, I want to ask how to seperate mitochondrial DNA and genome DNA, is it possible to use abyss?

Thanks,

Best regards,
Febri

[Shaun Jackman]

Hi, Febri. The mitochondrial DNA should be present at much higher coverage than the nuclear DNA. If you can get an estimate of the k-mer coverage of the mitochondrial DNA, you could set the coverage threshold parameters e and c to attempt to assemble the mitochondrial DNA but not the nuclear DNA, or alternatively take a subset of the reads that you think will give you deep enough coverage to assemble the mitochondrial DNA but not the nuclear DNA. High copy number nuclear repeats will also assemble. You'll then have to separate the nuclear repeat contigs from the mitochondrial contigs. That's trickier. If you have a related species with a mitochondrial reference you can align contigs to that reference.

Cheers,

Shaun

http://sjackman.ca

--
You received this message because you are subscribed to the Google Groups "ABySS" group.
To unsubscribe from this group and stop receiving emails from it, send an email to abyss-users...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.